PathogenSeq: TBDR

This tool processes raw sequence data to infer strain type and identify known drug resistance markers.

A stand alone version of this tool is now available and can now be run on linux or mac. Installation instructions can be found on GitHub and on the bioconda page.

This tool is for Research Use Only. Data and information provided through use of this tool are not intended for medical purpose or objective and should not be used for clinical diagnosis, patient management, or human clinical trials.

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Single nucleotide polymorphisms (SNPs) in coding regions are annotated using the reference amino acid, codon number and alternative amino acid (e.g. Ser315Thr in katG). SNPs in non-coding regions (i.e. RNA genes and intergenic regions) are annotated using the reference nucleotide, gene coordinate and alternative nucleotide (e.g. A1401G in rrs or C-37A in eis promoter). Indels are annotated using the reference VCF allele, gene coordinate and alternative VCF allele (e.g. T902TA insertion in katG).

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Summary

ID: 5cc551ba79bdf

Date: Sun Apr 28 08:11:18 2019

Strain: lineage4.3;lineage4.4.1;lineage4.6.1;lineage2.2.1.1

Drug-resistance: Sensitive

Drug¹ Resistance Supporting Mutations (frequency)

Isoniazid

Rifampicin

Ethambutol

Pyrazinamide

Streptomycin

Ethionamide

Fluoroquinolones

Amikacin

Capreomycin

Kanamycin

Lineage² Family Main Spoligotype RDS

lineage4.3 Euro-American (LAM) mainly-LAM None

lineage4.4.1 Euro-American (S-type) S;T None

lineage4.6.1 Euro-American (Uganda) T2 RD724

lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150

Mutations in candidate genes:

Gene	Chromosome Position	Mutation	Estimated fraction
gyrB	6319	c.1080G>C	1.000
gyrA	8480	c.1179C>T	1.000
gyrA	8486	c.1185T>C	1.000
gyrA	8507	c.1206C>T	1.000
rpoB	759571	c.-236C>A	1.000
rpoB	759606	c.-201T>C	1.000
rpoB	759629	c.-178T>C	1.000
rpoB	760181	c.375T>G	1.000
rpoB	760184	c.378A>G	1.000
rpoB	760196	c.390C>G	1.000
rpoB	760235	c.429T>C	1.000
rpoB	760283	c.477G>C	1.000
rpoB	760298	c.492G>C	1.000
rpoB	760340	c.534G>T	1.000
rpoB	760424	c.618C>G	1.000
rpoB	760646	c.840C>G	1.000
rpoB	760649	c.843G>C	1.000
rpoB	760655	c.849A>G	1.000
rpoB	760946	c.1140A>G	1.000
rpoB	760982	c.1176G>C	1.000
rpoB	760985	c.1179G>C	1.000
rpoB	760991	c.1185G>C	1.000
rpoB	761006	c.1200C>T	1.000
rpoB	761015	c.1209G>C	1.000
rpoB	761027	c.1221A>G	1.000
rpoB	761036	c.1230G>C	1.000
rpoB	761037	c.1231T>C	1.000
rpoB	761057	c.1251G>C	1.000
rpoB	761102	c.1296A>G	1.000
rpoB	761129	c.1323G>C	1.000
rpoB	761133	c.1327T>C	1.000
rpoB	761150	c.1344A>C	0.857
rpoB	761165	c.1359G>C	1.000
rpoB	761180	c.1374A>C	1.000
rpoB	761189	c.1383T>C	1.000
rpoB	761195	c.1389G>C	1.000
rpoB	761207	c.1401C>T	1.000
rpoB	761213	c.1407G>C	1.000
rpoB	761234	c.1428G>C	1.000
rpoB	761249	c.1443A>G	1.000
rpoB	761255	c.1449T>G	1.000
rpoB	761261	c.1455G>T	1.000
rpoB	761286	c.1480C>T	1.000
rpoB	761289	p.Ser495Ala	1.000
rpoB	761292	p.Val496Thr	1.000
rpoB	761300	c.1494G>C	1.000
rpoB	761327	c.1521A>G	1.000
rpoB	761558	c.1752C>G	1.000
rpoB	761579	c.1773G>C	1.000
rpoB	761942	c.2136C>T	1.000
rpoB	761948	c.2142G>C	1.000
rpoB	761954	c.2148C>G	1.000
rpoB	761999	c.2193G>C	1.000
rpoB	762014	c.2208C>T	1.000
rpoB	762017	c.2211A>G	1.000
rpoB	762206	c.2400C>G	1.000
rpoB	762212	c.2406G>C	1.000
rpoB	762233	c.2427G>C	1.000
rpoB	762254	c.2448T>G	1.000
rpoB	762257	c.2451C>G	1.000
rpoB	762260	c.2454C>T	1.000
rpoB	762284	c.2478G>C	1.000
rpoB	762293	c.2487T>C	1.000
rpoB	762863	c.3057T>C	1.000
rpoB	762929	c.3123G>T	1.000
rpoB	762962	c.3156C>T	1.000
rpoB	762971	c.3165G>A	1.000
rpoB	762989	c.3183G>C	1.000
rpoB	762995	c.3189G>T	1.000
rpoB	763028	c.3222T>C	1.000
rpoB	763031	c.3225T>G	1.000
rpoB	763040	c.3234C>G	1.000
rpoB	763070	c.3264T>C	1.000
rpoB	763115	c.3309T>C	1.000
rpoB	763136	c.3330C>T	1.000
rpoB	763148	c.3342G>C	1.000
rpoB	763158	c.3352C>T	1.000
rpoB	763166	c.3360A>G	1.000
rpoC	763351	c.-19T>C	1.000
rpoC	763352	c.-18T>A	1.000
rpoC	763402	c.33C>A	1.000
rpoC	763411	c.42T>G	1.000
rpoC	763414	c.45T>C	1.000
rpoC	763594	c.225C>T	1.000
rpoC	763603	c.234C>T	1.000
rpoC	763660	c.291T>G	1.000
rpoC	763675	c.306C>G	1.000
rpoC	763696	c.327T>C	1.000
rpoC	763702	c.333C>G	1.000
rpoC	763717	c.348T>C	1.000
rpoC	763723	c.354G>C	1.000
rpoC	763732	c.363C>G	1.000
rpoC	763741	c.372C>T	1.000
rpoC	763744	c.375G>C	1.000
rpoC	763765	c.396T>C	1.000
rpoC	763774	c.405G>C	1.000
rpoC	764140	c.771C>T	1.000
rpoC	764257	c.888G>C	1.000
rpoC	764665	c.1296C>G	1.000
rpoC	764713	c.1344G>C	1.000
rpoC	764716	c.1347G>C	1.000
rpoC	764752	c.1383G>C	1.000
rpoC	764764	c.1395T>C	1.000
rpoC	764797	c.1428G>C	1.000
rpoC	764803	c.1434C>T	1.000
rpoC	764809	c.1440C>T	1.000
rpoC	764815	c.1446A>G	1.000
rpoC	764827	c.1458G>C	1.000
rpoC	764858	c.1489T>C	1.000
rpoC	764888	c.1519T>C	1.000
rpoC	764893	c.1524T>C	1.000
rpoC	764911	c.1542A>G	1.000
rpoC	764932	c.1563C>A	0.947
rpoC	764935	c.1566T>C	1.000
rpoC	764948	c.1579T>C	1.000
rpoC	764968	c.1599T>C	1.000
rpoC	764995	c.1626C>G	1.000
rpoC	765047	c.1678T>C	1.000
rpoC	765055	c.1686C>G	1.000
rpoC	765103	c.1734G>T	1.000
rpoC	765478	c.2109T>C	1.000
rpoC	765499	c.2130C>G	1.000
rpoC	765508	c.2139C>G	1.000
rpoC	765529	c.2160C>T	1.000
rpoC	765541	c.2172C>G	1.000
rpoC	765553	c.2184C>T	1.000
rpoC	765556	c.2187G>C	1.000
rpoC	765559	c.2190G>C	1.000
rpoC	765580	c.2211G>C	1.000
rpoC	765613	p.His748Gln	1.000
rpoC	765658	c.2289C>T	1.000
rpoC	765700	c.2331T>C	1.000
rpoC	765734	c.2365T>C	1.000
rpoC	765739	c.2370G>T	1.000
rpoC	765751	c.2382C>G	1.000
rpoC	765753	p.Asp795Ala	1.000
rpoC	765772	c.2403C>G	1.000
rpoC	765784	c.2415C>G	1.000
rpoC	765793	c.2424C>G	1.000
rpoC	765796	c.2427C>T	1.000
rpoC	765826	c.2457T>C	1.000
rpoC	765835	c.2466C>T	1.000
rpoC	765883	c.2514C>G	1.000
rpoC	765886	c.2517C>G	1.000
rpoC	765892	c.2523T>C	1.000
rpoC	765967	c.2598C>T	1.000
rpoC	765979	c.2610C>G	1.000
rpoC	765982	c.2613C>T	1.000
rpoC	765994	c.2625A>T	1.000
rpoC	766009	c.2640G>C	1.000
rpoC	766010	c.2641T>A	1.000
rpoC	766021	c.2652G>C	1.000
rpoC	766027	c.2658G>C	1.000
rpoC	766043	p.Gln892Glu	1.000
rpoC	766054	c.2685C>G	1.000
rpoC	766061	p.Val898Ile	1.000
rpoC	766408	c.3039C>T	1.000
rpoC	766426	c.3057C>T	1.000
rpoC	766447	c.3078T>C	1.000
rpoC	766459	c.3090G>T	0.923
rpoC	766483	c.3114G>C	1.000
rpoC	766484	p.Val1039Ile	1.000
rpoC	766492	c.3123T>C	1.000
rpoC	766495	c.3126C>T	1.000
rpoC	766522	c.3153C>G	1.000
rpoC	766528	c.3159T>C	1.000
rpoC	766531	c.3162G>T	1.000
rpoC	766540	p.Asp1057Glu	1.000
rpoC	766549	c.3180G>C	1.000
rpoC	766726	c.3357T>C	1.000
rpoC	766738	c.3369G>C	1.000
rpoC	766801	c.3432C>G	1.000
rpoC	766804	c.3435A>G	1.000
rpoC	766861	c.3492G>C	1.000
rpoC	766864	c.3495G>C	1.000
rpoC	766894	c.3525T>C	1.000
rpoC	766895	c.3526T>C	1.000
rpoC	766900	c.3531T>C	1.000
rpoC	766903	c.3534C>T	1.000
rpoC	766918	c.3549C>T	1.000
rpoC	766933	c.3564A>G	1.000
rpoC	766945	c.3576A>G	1.000
rpoC	766963	c.3594T>C	1.000
rpoC	766972	c.3603G>C	1.000
rpoC	766996	c.3627C>T	1.000
rpoC	767032	c.3663G>T	1.000
rpoC	767035	c.3666G>T	1.000
rpoC	767059	c.3690T>G	1.000
rpoC	767062	c.3693C>A	1.000
rpoC	767098	c.3729T>C	1.000
rpoC	767119	c.3750A>G	1.000
rpoC	767134	c.3765C>A	1.000
rpoC	767158	c.3789T>C	0.923
rpoC	767167	c.3798C>G	1.000
rpoC	767180	p.Ala1271Gln	1.000
rpoC	767191	c.3822C>G	1.000
rpsL	781649	c.90T>C	1.000
rpsL	781655	c.96T>C	1.000
rpsL	781700	c.141G>C	1.000
rpsL	781703	c.144G>T	1.000
rpsL	781715	c.156T>C	1.000
rpsL	781728	c.169T>C	1.000
rpsL	781736	c.177T>C	1.000
rpsL	781742	c.183C>T	1.000
rpsL	781754	c.195G>C	1.000
rpsL	781760	c.201T>C	1.000
rpsL	781769	c.210G>A	1.000
rpsL	781772	c.213C>T	1.000
rpsL	781808	c.249C>T	1.000
rpsL	781811	c.252C>T	1.000
rpsL	781832	c.273T>C	1.000
rpsL	781838	c.279G>C	1.000
rpsL	781841	c.282C>G	1.000
rpsL	781865	c.306G>C	1.000
rpsL	781868	c.309T>C	1.000
rpsL	781871	c.312G>C	1.000
rpsL	781877	c.318T>C	1.000
rpsL	781892	c.333A>G	1.000
rpsL	781898	c.339A>T	1.000
rpsL	781916	c.357T>C	1.000
rpsL	781929	p.Gly124Ser	1.000
rplC	800814	c.6A>G	1.000
rplC	800817	c.9A>T	1.000
rrs	1471923	r.78t>c	1.000
rrs	1471925	r.80t>c	1.000
rrs	1471932	r.87a>g	1.000
rrs	1471934	r.89a>g	1.000
rrs	1471969	r.124t>c	1.000
rrs	1471970	r.125g>a	1.000
rrs	1472028	r.183a>t	1.000
rrs	1472029	r.184c>t	1.000
rrs	1472030	r.185g>t	1.000
rrs	1472031	r.186g>a	1.000
rrs	1472034	r.189t>c	1.000
rrs	1472044	r.199g>t	1.000
rrs	1472053	r.208agc>a	1.000
rrs	1472061	r.216a>t	1.000
rrs	1472075	r.230a>g	1.000
rrs	1472108	r.263c>t	1.000
rrs	1472969	r.1124a>g	1.000
rrs	1472970	r.1125c>g	1.000
rrs	1472977	r.1132g>c	1.000
rrs	1472978	r.1133t>c	1.000
rrs	1473105	r.1260g>a	1.000
rrs	1473120	r.1275c>ct	0.850
rrs	1473123	r.1278a>t	0.947
rrs	1473145	r.1300c>t	1.000
rrs	1473166	r.1321g>a	1.000
rrs	1473290	r.1445c>t	1.000
rrl	1473668	r.11c>t	1.000
rrl	1473756	r.99g>a	1.000
rrl	1473758	r.101g>t	1.000
rrl	1473806	r.149c>t	1.000
rrl	1473877	r.220g>a	1.000
rrl	1473898	r.241c>t	1.000
rrl	1473899	r.242a>c	1.000
rrl	1473938	r.281g>a	1.000
rrl	1473939	r.282c>t	1.000
rrl	1473943	r.286g>t	1.000
rrl	1473986	r.329t>c	1.000
rrl	1473995	r.338g>t	1.000
rrl	1474001	r.344c>t	1.000
rrl	1474009	r.352a>g	1.000
rrl	1474012	r.355c>t	1.000
rrl	1474044	r.387c>t	1.000
rrl	1474054	r.397t>c	1.000
rrl	1474093	r.436g>t	1.000
rrl	1474099	r.442g>a	1.000
rrl	1474103	r.446a>t	1.000
rrl	1474140	r.483c>t	1.000
rrl	1474151	r.494c>t	1.000
rrl	1474181	r.524c>t	1.000
rrl	1474249	r.592g>t	1.000
rrl	1474291	r.634tttcctctccggagga>t	1.000
rrl	1474356	r.699t>c	1.000
rrl	1474362	r.705a>g	1.000
rrl	1474376	r.719t>c	1.000
rrl	1474639	r.982g>a	1.000
rrl	1474794	r.1137c>t	1.000
rrl	1474812	r.1155g>a	1.000
rrl	1474823	r.1166c>t	1.000
rrl	1474831	r.1174a>g	1.000
rrl	1474904	r.1247g>a	1.000
rrl	1474956	r.1299c>t	1.000
rrl	1474960	r.1303c>g	1.000
rrl	1474962	r.1305t>c	1.000
rrl	1474963	r.1306g>t	1.000
rrl	1474964	r.1307t>a	1.000
rrl	1474965	r.1308g>c	1.000
rrl	1474970	r.1313g>a	1.000
rrl	1475006	r.1349a>t	1.000
rrl	1475013	r.1356g>a	1.000
rrl	1475061	r.1404c>t	1.000
rrl	1475088	r.1431a>t	1.000
rrl	1475199	r.1542g>a	1.000
rrl	1475206	r.1549c>t	0.900
rrl	1475291	r.1634a>c	1.000
rrl	1475313	r.1656g>a	1.000
rrl	1475315	r.1658a>t	1.000
rrl	1475355	r.1698c>t	1.000
rrl	1475369	r.1712g>t	1.000
rrl	1475402	r.1745c>t	1.000
rrl	1475419	r.1762c>t	1.000
rrl	1475436	r.1779c>t	1.000
rrl	1475483	r.1826c>t	1.000
rrl	1475505	r.1848g>a	1.000
rrl	1475526	r.1869c>a	1.000
rrl	1475573	r.1916g>a	1.000
rrl	1475599	r.1942a>g	1.000
rrl	1475608	r.1951t>c	1.000
rrl	1475642	r.1985t>c	1.000
rrl	1475657	r.2000a>g	1.000
rrl	1475659	r.2002g>t	1.000
rrl	1475758	r.2101ac>a	1.000
rrl	1475763	r.2106c>t	1.000
rrl	1475765	r.2108ag>a	1.000
rrl	1475881	r.2224t>c	1.000
rrl	1476131	r.2474c>t	1.000
rrl	1476183	r.2526a>c	1.000
rrl	1476214	r.2557g>t	1.000
rrl	1476215	r.2558c>t	1.000
rrl	1476224	r.2567a>g	1.000
rrl	1476281	r.2624t>c	1.000
rrl	1476628	r.2971t>a	1.000
rrl	1476689	r.3032a>t	1.000
rrl	1476690	r.3033c>t	1.000
rrl	1476693	r.3036g>a	1.000
rrl	1476695	r.3038t>a	1.000
rrl	1476716	r.3059a>c	1.000
inhA	1674636	c.435C>G	1.000
inhA	1674660	c.459G>C	1.000
rpsA	1833589	c.48A>T	1.000
rpsA	1833595	c.54T>C	1.000
rpsA	1833610	c.69C>T	1.000
rpsA	1833661	c.120A>G	1.000
rpsA	1833667	c.126C>G	1.000
rpsA	1833724	c.183C>G	1.000
rpsA	1833727	c.186G>C	1.000
rpsA	1833742	c.201A>G	1.000
rpsA	1833745	c.204G>C	1.000
rpsA	1833748	c.207C>G	1.000
rpsA	1833772	c.231C>T	1.000
rpsA	1833787	c.246C>G	1.000
rpsA	1833790	c.249T>C	1.000
rpsA	1833808	c.267G>C	1.000
rpsA	1833811	c.270G>T	1.000
rpsA	1833835	c.294C>T	1.000
rpsA	1833838	c.297G>C	1.000
rpsA	1833841	c.300C>G	1.000
rpsA	1833847	c.306C>G	1.000
rpsA	1833856	c.315A>G	1.000
rpsA	1833868	c.327C>T	1.000
rpsA	1833874	c.333T>C	1.000
rpsA	1833928	c.387G>C	1.000
rpsA	1833940	c.399C>G	1.000
rpsA	1833971	c.430C>T	1.000
rpsA	1833979	c.438T>C	1.000
rpsA	1834000	c.459G>C	1.000
rpsA	1834021	c.480C>T	1.000
rpsA	1834030	c.489C>G	1.000
rpsA	1834222	c.681T>C	1.000
rpsA	1834249	c.708T>C	1.000
rpsA	1834339	c.798C>T	1.000
rpsA	1834639	c.1098T>C	1.000
rpsA	1834780	c.1239A>G	1.000
rpsA	1834789	c.1248T>C	1.000
rpsA	1834792	c.1251G>C	1.000
ahpC	2726638	p.Ala149Val	1.000
ahpC	2726645	c.453C>G	1.000
ahpC	2726657	c.465A>C	1.000
ahpC	2726669	p.Asp159Glu	1.000
ahpC	2726672	c.480G>A	1.000
ahpC	2726675	c.483A>G	1.000
ahpC	2726681	c.489A>C	1.000
ahpC	2726693	c.501C>A	1.000
ahpC	2726696	c.504C>G	1.000
ahpC	2726717	c.525A>G	1.000
thyX	3067316	c.630T>C	1.000
thyX	3067325	c.621T>C	1.000
thyX	3067349	c.597C>G	1.000
thyX	3067355	c.591T>G	1.000
thyX	3067367	c.579C>G	1.000
thyX	3067391	c.555C>G	1.000
thyX	3067394	c.552C>G	1.000
thyX	3067898	p.Asp16Glu	1.000
thyA	3073953	c.519A>G	1.000
thyA	3073977	c.495T>C	1.000
thyA	3073989	c.483A>G	1.000
thyA	3074001	c.471G>C	1.000
thyA	3074004	c.468A>G	1.000
embC	4241107	c.1245G>C	1.000
embC	4241131	c.1269G>A	1.000
embC	4241140	c.1278A>G	1.000
embC	4241146	c.1284C>G	1.000
embC	4241158	c.1296T>G	1.000
embC	4241161	c.1299C>G	1.000
embC	4241162	c.1300T>C	1.000
embA	4245137	c.1905T>C	1.000
embA	4245153	p.Ile641Val	1.000
embB	4248169	c.1656C>G	1.000
embB	4248172	c.1659G>C	1.000
embB	4248220	c.1707A>T	1.000
embB	4248241	c.1728C>T	1.000
embB	4249469	p.Leu986Met	1.000
embB	4249486	c.2973T>G	1.000

Analysis pipeline specifications

TBProfiler Version: 2.1.1

Analysis	Program
Mapping	bwa
Variant Calling	BCFtools

Log

Drug Details

The estimated accuracy of drug resistance predictions is:

Drug¹	Sensitivity (%)	Specificity (%)
Isoniazid	92.8 (89.9-95.7)	100 (100-100)
Rifampicin	96.2 (93.9-98.5)	98.1 (96.8-99.4)
Ethambutal	88.7 (83.6-93.8)	81.7 (77.6-85.8)
Pyrazinamide	70.9 (62.4-79.4)	93.9 (90.6-97.2)
Streptomycin	87.1 (82.7-91.5)	89.7 (86.0-93.4)
Ethionamide	73.6 (66.7-80.5)	93.3 (89.6-97.0)
Moxifloxacin	60.0 (29.6-90.4)	68.7 (52.6-84.8)
Ofloxacin	85.5 (79.1-91.9)	94.9 (91.8-98.0)
Amikacin	82.9 (74.4-91.4)	98.3 (96.0-100)
Capreomycin	60.7 (50.6-70.8)	90.7 (87.2-94.2)
Kanamycin	87.3 (81.3-93.3)	93.4 (89.9-96.9)
Para-aminosalisylic acid	Not determined	Not determined
Linezolid	Not determined	Not determined
Clofazimine	Not determined	Not determined
Bedaquiline	Not determined	Not determined
Multi drug resistance	91.2 (87.8-94.6)	98.4 (97.2-99.6)
Extremely drug resistance	75.9 (64.5-87.3)	98.4 (97.3-99.5)

Lineages

Lineage²	Location	Strain	RD type
lineage1	Indo-Oceanic	EAI	RD239
lineage1.1	Indo-Oceanic	EAI3;EAI4;EAI5;EAI6	RD239
lineage1.1.1	Indo-Oceanic	EAI4;EAI5	RD239
lineage1.1.1.1	Indo-Oceanic	EAI4;ZERO	RD239
lineage1.1.2	Indo-Oceanic	EAI3;EAI5	RD239
lineage1.1.3	Indo-Oceanic	EAI6	RD239
lineage1.2	Indo-Oceanic	EAI1;EAI2	RD239
lineage1.2.1	Indo-Oceanic	EAI2	RD239
lineage1.2.2	Indo-Oceanic	EAI1	RD239
lineage2	East-Asian	Beijing	RD105
lineage2.1	East-Asian (non-Beijing)	None	None
lineage2.2	East-Asian (Beijing)	Beijing-RD207	RD105;RD207
lineage2.2.2	East-Asian (Beijing)	Beijing-RD105/RD207	RD105;RD207
lineage2.2.1	East-Asian (Beijing)	Beijing-RD181	RD105;RD207;RD181
lineage2.2.1.2	East-Asian (Beijing)	Beijing-RD142	RD105;RD207;RD181;RD142
lineage2.2.1.1	East-Asian (Beijing)	Beijing-RD150	RD105;RD207;RD181;RD150
lineage3	East-African-Indian	CAS	RD750
lineage3.1	East-African-Indian	Non-CAS1-Delhi	RD750
lineage3.1.1	East-African-Indian	CAS1-Kili	RD750
lineage3.1.2	East-African-Indian	CAS;CAS2	RD750
lineage3.1.2.1	East-African-Indian	CAS2	RD750
lineage3.1.2.2	East-African-Indian	CAS	RD750
lineage4	Euro-American	LAM;T;S;X;H	None
lineage4.1	Euro-American	T;X;H	None
lineage4.1.2	Euro-American (X-type)	T;H	None
lineage4.1.2.1	Euro-American (X-type)	T1;H1	RD182
lineage4.1.1	Euro-American (X-type)	X1;X2;X3	None
lineage4.1.1.2	Euro-American (X-type)	X1	None
lineage4.1.1.1	Euro-American (X-type)	X2	RD183
lineage4.1.1.3	Euro-American (Haarlem)	X1;X3	RD193
lineage4.2	Euro-American	H;T;LAM	None
lineage4.2.2	Euro-American (Ural)	T;LAM7-TUR	None
lineage4.2.2.1	Euro-American	LAM7-TUR	None
lineage4.2.1	Euro-American (TUR)	H3;H4	None
lineage4.3	Euro-American (LAM)	mainly-LAM	None
lineage4.3.1	Euro-American (LAM)	LAM9	None
lineage4.3.3	Euro-American (LAM)	LAM;T	RD115
lineage4.3.4	Euro-American (LAM)	LAM	RD174
lineage4.3.4.1	Euro-American (LAM)	LAM1;LAM2	RD174
lineage4.3.4.2	Euro-American (LAM)	LAM1;LAM4;LAM11	RD174
lineage4.3.4.2.1	Euro-American (LAM)	LAM11	RD174
lineage4.3.2	Euro-American (LAM)	LAM3	None
lineage4.3.2.1	Euro-American (LAM)	LAM3	RD761
lineage4.4	Euro-American	S;T	None
lineage4.4.2	Euro-American	T1;T2	None
lineage4.4.1	Euro-American (S-type)	S;T	None
lineage4.4.1.2	Euro-American	T1	None
lineage4.4.1.1	Euro-American	S;Orphans	None
lineage4.5	Euro-American	H;T	RD122
lineage4.6	Euro-American	T;LAM	None
lineage4.6.1	Euro-American (Uganda)	T2	RD724
lineage4.6.1.1	Euro-American	T2-Uganda	RD724
lineage4.6.1.2	Euro-American	T2	RD724
lineage4.6.2	Euro-American	T;LAM	RD726
lineage4.6.2.1	Euro-American	T3	RD726
lineage4.6.2.2	Euro-American (Cameroon)	LAM10-CAM	RD726
lineage4.7	Euro-American (mainly T)	T1;T5	None
lineage4.8	Euro-American (mainly T)	T1;T2;T3;T5	RD219
lineage4.9	Euro-American (H37Rv-like)	T1	None
lineage5	West-Africa 1	AFRI_2;AFRI_3	RD711
lineage6	West-Africa 2	AFRI_1	RD702
lineage7	Lineage 7	None	None
lineageBOV	M. bovis	BOV_1;BOV_2	None

Citations

1. Coll F, et al. Rapid determination of anti-tuberculosis drug resistance from whole genome sequences. Genome Medicine (in press)
2. Coll F, et al. A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. Nature Communications 2014.

Disclaimer

This tool is for Research Use Only and is offered free for use. The London School of Hygiene and Tropical Medicine shall have no liability for any loss or damages of any kind, however sustained relating to the use of this tool.

Drug¹	Resistance	Supporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
Streptomycin
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage²	Family	Main Spoligotype	RDS
lineage4.3	Euro-American (LAM)	mainly-LAM	None
lineage4.4.1	Euro-American (S-type)	S;T	None
lineage4.6.1	Euro-American (Uganda)	T2	RD724
lineage2.2.1.1	East-Asian (Beijing)	Beijing-RD150	RD105;RD207;RD181;RD150